The symbiosis between Sphagnum mosses and cyanobacteria has long been recognized (Limpricht, 1890) and has been implicated in improved moss growth. This together with evidence form other plant - cyanobacteria symbioses suggest that this is not just a symbiosis (interacting species), but perhaps a mutualsitc interaction – thereby benefiting both interacting speices. To investigate this further, Colleen Hulsey and Megan Gable conducted a numer of experiments to investigate the growth consequences of cyanobacteria and sphagnum symbiosis on growth patterns at differing pH. conditions.
*Experimental conditions & design +conducted on 08/09/2018 +plants pH nitrogen depleted for 2 weeks prior to start +experiment ran for 2 weeks +condition 1: Nitrogen (N), 6 replicates -N, 2 replicates for low N (5mL/L NaNO3– Mm?) +Condition 2: pH, 3.5, 5.5, 8.5 +speices: Sphagnum fallax MN alone, Nostoc muscorum 1037 alone, both species together +amounts: 1 moss capitulum, 0.1g cyanobacteria +3 - 12 well plates, 2 ml liquid medium per well.
*Measurements +fluorcam: area_mm2, QY_max (initial, weekly, final) +pH initial, pH weekly, pH final +weight beginning and end after water removed with centrifugation
*tests +simple scatter and boxplots to view realtionship
library(tidyverse)
#knitr by default will set the working directory to the source file location
#setwd("~/Documents/Manuscripts:data/Symbiosis_study_2018")
dat1 <- read_csv("fallax_cyano_symbiosis_colleen_10_01_2018.csv") %>% mutate(delta_weight = delta_weight_g *1000)
names(dat1)
## [1] "Sample_well" "component_measured" "condition"
## [4] "initial_pH" "final_pH" "initial_weight_g"
## [7] "final_weight_g" "delta_weight_g" "delta_weight"
summary(dat1)
## Sample_well component_measured condition initial_pH
## Length:72 Length:72 Length:72 Min. :3.500
## Class :character Class :character Class :character 1st Qu.:3.500
## Mode :character Mode :character Mode :character Median :5.500
## Mean :5.833
## 3rd Qu.:8.500
## Max. :8.500
##
## final_pH initial_weight_g final_weight_g delta_weight_g
## Min. :3.700 Min. :0.00140 Min. :0.01430 Min. :-0.03560
## 1st Qu.:5.800 1st Qu.:0.01342 1st Qu.:0.04083 1st Qu.: 0.01082
## Median :6.200 Median :0.09345 Median :0.09570 Median : 0.03030
## Mean :6.117 Mean :0.06677 Mean :0.10127 Mean : 0.03766
## 3rd Qu.:6.700 3rd Qu.:0.10622 3rd Qu.:0.15368 3rd Qu.: 0.06940
## Max. :7.440 Max. :0.12040 Max. :0.22060 Max. : 0.11090
## NA's :12 NA's :12 NA's :12
## delta_weight
## Min. :-35.60
## 1st Qu.: 10.82
## Median : 30.30
## Mean : 37.66
## 3rd Qu.: 69.40
## Max. :110.90
##
dim(dat1)
## [1] 72 9
Fig. 1: 2018 data, change in growth (initial weight (wt) - final wt among the two symbiotic partners alone and when added togather but grown seperately (_seperate) and when grown together in same well (_symbiosis). Cyano in symbiosis includes, endophytes, epiphytes and free living cyano. Data incuded all pH conditions
Fig. 2: 2018 data, change in growth among interacting partners faceted by starting pH condiiton. Measured components as described in fig. 1
Fig. 3: 2018 data, total well biomass change from experiment start to finish. Includes moss + cyano endophyte and free living cyanobacteria not attached to plant
## Warning: Removed 12 rows containing non-finite values (stat_boxplot).
## Warning: Removed 12 rows containing missing values (geom_point).
Fig. 4: 2018 data, change in pH change as measured by (final - initial values)
## Warning: Removed 12 rows containing non-finite values (stat_boxplot).
## Warning: Removed 12 rows containing missing values (geom_point).
Fig. 5: 2018 data, absolute value of pH change as measured by (final - initial values)
need experimental details here…
dat2 <- read_csv("fallax_cyano_symbiosis_allyssa_colleen_2017.csv")
dat3 <- dat2 %>% filter(pH == 3.5 | pH == 5.5 | pH == 8.5)
names(dat3)
## [1] "condition" "replicate" "pH" "plate"
## [5] "well" "weight_initial" "weight_final" "delta_weight"
summary(dat3)
## condition replicate pH plate
## Length:72 Min. :1.0 Min. :3.500 Min. :1
## Class :character 1st Qu.:2.0 1st Qu.:3.500 1st Qu.:3
## Mode :character Median :3.5 Median :5.500 Median :5
## Mean :3.5 Mean :5.833 Mean :5
## 3rd Qu.:5.0 3rd Qu.:8.500 3rd Qu.:7
## Max. :6.0 Max. :8.500 Max. :9
## NA's :18 NA's :18
## well weight_initial weight_final delta_weight
## Min. : 1.000 Min. : 3.11 Min. : 8.67 Min. :-21.330
## 1st Qu.: 3.000 1st Qu.:21.73 1st Qu.: 29.20 1st Qu.: 8.562
## Median : 6.500 Median :30.00 Median : 46.91 Median : 23.870
## Mean : 6.333 Mean :33.72 Mean : 64.98 Mean : 32.358
## 3rd Qu.: 9.000 3rd Qu.:40.02 3rd Qu.: 96.84 3rd Qu.: 46.220
## Max. :12.000 Max. :87.22 Max. :177.43 Max. :127.830
## NA's :18 NA's :18 NA's :18
dim(dat3)
## [1] 72 8
Fig. 6: 2017 data, change in growth (initial weight (wt) - final wt among the two symbiotic partners alone, when added togather but grown seperately (_seperate) and when grown together in same well (_symbiosis). Conditions aggregated over pH
Fig. 7: 2017 data, change in growth (initial weight (wt) - final wt among the two symbiotic partners alone, when added togather but grown seperately (_seperate) and when grown together in same well (_symbiosis). Similar to Fig. 6 except faceted by pH
Fig. 8: Combined 2018 and 2017 data for change in growth (initial weight (wt) - among the two symbiotic partners alone, when added togather but grown seperately (_seperate) and when grown together in same well (_symbiosis). Data is faceted by pH
Specifically testing if cyano and moss grown alone, increased in growth at a different rate than when grown together in smbiosis.
2017 Sphagnum-Cyano Import
2017 Summary statistics and graphs
Confirms similar info to 2018 data. Cyano & moss grown together have higher weight than grown separate or grown alone. Higher pHs correspond to produce higher growth with the symbiotic relationship increasing growth response as pH increases.
2017 Two-way ANOVA
## Df Sum Sq Mean Sq F value Pr(>F)
## condition 3 20854 6951 9.251 4.05e-05 ***
## pH 2 8810 4405 5.862 0.00473 **
## condition:pH 6 2464 411 0.546 0.77075
## Residuals 60 45086 751
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = delta_weight ~ condition + pH + condition:pH, data = tri.2017)
##
## $condition
## diff
## Cyanobacteria_moss_seperate-cyano_alone 23.38444
## Cyanobacteria_moss_symbiosis-cyano_alone 45.84889
## moss_alone-cyano_alone 11.11278
## Cyanobacteria_moss_symbiosis-Cyanobacteria_moss_seperate 22.46444
## moss_alone-Cyanobacteria_moss_seperate -12.27167
## moss_alone-Cyanobacteria_moss_symbiosis -34.73611
## lwr
## Cyanobacteria_moss_seperate-cyano_alone -0.761391
## Cyanobacteria_moss_symbiosis-cyano_alone 21.703053
## moss_alone-cyano_alone -13.033058
## Cyanobacteria_moss_symbiosis-Cyanobacteria_moss_seperate -1.681391
## moss_alone-Cyanobacteria_moss_seperate -36.417502
## moss_alone-Cyanobacteria_moss_symbiosis -58.881947
## upr
## Cyanobacteria_moss_seperate-cyano_alone 47.53028
## Cyanobacteria_moss_symbiosis-cyano_alone 69.99472
## moss_alone-cyano_alone 35.25861
## Cyanobacteria_moss_symbiosis-Cyanobacteria_moss_seperate 46.61028
## moss_alone-Cyanobacteria_moss_seperate 11.87417
## moss_alone-Cyanobacteria_moss_symbiosis -10.59028
## p adj
## Cyanobacteria_moss_seperate-cyano_alone 0.0610500
## Cyanobacteria_moss_symbiosis-cyano_alone 0.0000289
## moss_alone-cyano_alone 0.6191255
## Cyanobacteria_moss_symbiosis-Cyanobacteria_moss_seperate 0.0771172
## moss_alone-Cyanobacteria_moss_seperate 0.5396394
## moss_alone-Cyanobacteria_moss_symbiosis 0.0018777
##
## $pH
## diff lwr upr p adj
## pH_5.5-pH_3.5 14.10375 -4.913481 33.12098 0.1842030
## pH_8.5-pH_3.5 27.08708 8.069852 46.10431 0.0031737
## pH_8.5-pH_5.5 12.98333 -6.033898 32.00056 0.2367043
2017 Testing ANOVA assumptions
##
## Shapiro-Wilk normality test
##
## data: tri2017.residuals
## W = 0.96343, p-value = 0.03459
## Loading required package: carData
##
## Attaching package: 'car'
## The following object is masked from 'package:dplyr':
##
## recode
## The following object is masked from 'package:purrr':
##
## some
## Levene's Test for Homogeneity of Variance (center = median)
## Df F value Pr(>F)
## group 11 2.0352 0.04026 *
## 60
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
2017 Nonparametric Tests
## Coefficient covariances computed by hccm()
##
## DV: delta_weight
## Observations: 72
## D: 1
## MS total: 438
2017 Normality and Variance correction
## Warning in sqrt(weight): NaNs produced
##
## Call:
## lm(formula = logvars ~ logmeans)
##
## Residuals:
## 1 2 3
## -0.0006837 0.0018373 -0.0011536
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.698544 0.012165 57.42 0.01109 *
## logmeans 1.508940 0.008162 184.87 0.00344 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.002275 on 1 degrees of freedom
## Multiple R-squared: 1, Adjusted R-squared: 0.9999
## F-statistic: 3.418e+04 on 1 and 1 DF, p-value: 0.003444
## [1] 0.24553
2017 Testing ANOVA - Square root
## Df Sum Sq Mean Sq F value Pr(>F)
## condition 3 95.63 31.88 7.630 0.000262 ***
## pH 2 55.15 27.58 6.601 0.002823 **
## condition:pH 6 22.00 3.67 0.878 0.517890
## Residuals 51 213.08 4.18
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 9 observations deleted due to missingness
##
## Shapiro-Wilk normality test
##
## data: tri2017.transresiduals
## W = 0.98782, p-value = 0.7902
## Levene's Test for Homogeneity of Variance (center = median)
## Df F value Pr(>F)
## group 11 2.609 0.01021 *
## 51
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Testing ANOVA - Exp Transform
## Df Sum Sq Mean Sq F value Pr(>F)
## condition 3 4.334 1.4447 8.339 0.000131 ***
## pH 2 2.228 1.1139 6.429 0.003236 **
## condition:pH 6 0.897 0.1496 0.863 0.528150
## Residuals 51 8.836 0.1733
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 9 observations deleted due to missingness
##
## Shapiro-Wilk normality test
##
## data: tri2017.transresiduals2
## W = 0.98278, p-value = 0.5233
## Levene's Test for Homogeneity of Variance (center = median)
## Df F value Pr(>F)
## group 11 2.1987 0.02899 *
## 51
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
2018 Spagnum_Cyano Import
## 'data.frame': 48 obs. of 3 variables:
## $ pH : num 3.5 3.5 3.5 3.5 5.5 5.5 5.5 5.5 8.5 8.5 ...
## $ condition : Factor w/ 6 levels "cyano_alone",..: 5 5 5 5 5 5 5 5 5 5 ...
## $ delta_weight: num 10.3 11 32 77.3 19.3 23.6 49.2 50 45.5 28.2 ...
## 'data.frame': 48 obs. of 3 variables:
## $ pH : Factor w/ 3 levels "pH_3.5","pH_5.5",..: 1 1 1 1 2 2 2 2 3 3 ...
## $ condition : Factor w/ 4 levels "moss_alone","cyano_alone",..: 1 1 1 1 1 1 1 1 1 1 ...
## $ delta_weight: num 10.3 11 32 77.3 19.3 23.6 49.2 50 45.5 28.2 ...
##
## moss_alone cyano_alone Cyanobacteria_moss_symbiosis
## pH_3.5 4 4 4
## pH_5.5 4 4 4
## pH_8.5 4 4 4
##
## Cyanobacteria_moss_seperate
## pH_3.5 4
## pH_5.5 4
## pH_8.5 4
2018 Summary statistics and graphs
Data suggests that growth is driven by both condition and pH and that condition influences responses to pH. Graphs show support for the idea that at higher pH there is increased growth of Sphagnum, indicative of a symbiotic relationship.
2018 Two-way ANOVA
## Df Sum Sq Mean Sq F value Pr(>F)
## condition 3 11694 3898 5.216 0.00429 **
## pH 2 32248 16124 21.577 6.93e-07 ***
## condition:pH 6 11846 1974 2.642 0.03159 *
## Residuals 36 26902 747
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = delta_weight ~ condition + pH + condition:pH, data = tri.2018)
##
## $condition
## diff
## cyano_alone-moss_alone -11.858333
## Cyanobacteria_moss_symbiosis-moss_alone 26.866667
## Cyanobacteria_moss_seperate-moss_alone 20.800000
## Cyanobacteria_moss_symbiosis-cyano_alone 38.725000
## Cyanobacteria_moss_seperate-cyano_alone 32.658333
## Cyanobacteria_moss_seperate-Cyanobacteria_moss_symbiosis -6.066667
## lwr
## cyano_alone-moss_alone -41.915110
## Cyanobacteria_moss_symbiosis-moss_alone -3.190110
## Cyanobacteria_moss_seperate-moss_alone -9.256777
## Cyanobacteria_moss_symbiosis-cyano_alone 8.668223
## Cyanobacteria_moss_seperate-cyano_alone 2.601556
## Cyanobacteria_moss_seperate-Cyanobacteria_moss_symbiosis -36.123444
## upr
## cyano_alone-moss_alone 18.19844
## Cyanobacteria_moss_symbiosis-moss_alone 56.92344
## Cyanobacteria_moss_seperate-moss_alone 50.85678
## Cyanobacteria_moss_symbiosis-cyano_alone 68.78178
## Cyanobacteria_moss_seperate-cyano_alone 62.71511
## Cyanobacteria_moss_seperate-Cyanobacteria_moss_symbiosis 23.99011
## p adj
## cyano_alone-moss_alone 0.7140984
## Cyanobacteria_moss_symbiosis-moss_alone 0.0937375
## Cyanobacteria_moss_seperate-moss_alone 0.2614148
## Cyanobacteria_moss_symbiosis-cyano_alone 0.0071606
## Cyanobacteria_moss_seperate-cyano_alone 0.0288313
## Cyanobacteria_moss_seperate-Cyanobacteria_moss_symbiosis 0.9476697
##
## $pH
## diff lwr upr p adj
## pH_5.5-pH_3.5 33.6875 10.063467 57.31153 0.0036631
## pH_8.5-pH_3.5 63.4500 39.825967 87.07403 0.0000004
## pH_8.5-pH_5.5 29.7625 6.138467 53.38653 0.0107795
Main question is if cyano_alone and moss_alone grew at different rate than cyano_moss_symbiosis. Graphs show that cyano_moss_symbiosis grows more at high pH, but Tukey HSD suggests that at p-value < 0.05, cyano_moss_symbiosis is only significantly different from cyano_alone and that cyano_moss_separated is different from cyano_alone. This suggests that cyano grows better when in contact or proximity with moss. cyano_moss_separate is nearly significantly different from moss alone (p-value = 0.09 at p-value < 0.1) perhaps indicating that moss benefits marginally from proximity to cyano (hormogonia?), but not as much as cyano benefits from proximity of moss.
2018 Testing ANOVA assumptions
##
## Shapiro-Wilk normality test
##
## data: tri2018.residuals
## W = 0.9626, p-value = 0.1285
##
## Bartlett test of homogeneity of variances
##
## data: delta_weight by interaction(condition, pH)
## Bartlett's K-squared = 13.881, df = 11, p-value = 0.2396
## Levene's Test for Homogeneity of Variance (center = median)
## Df F value Pr(>F)
## group 11 1.4796 0.1821
## 36
All Data Summary Stats
ANOVAs with factor(year)
## Df Sum Sq Mean Sq F value Pr(>F)
## year 1 2465 2465 2.168 0.144
## condition 3 31575 10525 9.256 1.61e-05 ***
## year:condition 3 974 325 0.285 0.836
## Residuals 112 127356 1137
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = delta_weight ~ year + condition + year:condition, data = alldata)
##
## $year
## diff lwr upr p adj
## 2018-2017 9.252222 -3.197809 21.70225 0.1437031
##
## $condition
## diff
## Cyanobacteria_moss_seperate-cyano_alone 27.09400
## Cyanobacteria_moss_symbiosis-cyano_alone 42.99933
## moss_alone-cyano_alone 11.41100
## Cyanobacteria_moss_symbiosis-Cyanobacteria_moss_seperate 15.90533
## moss_alone-Cyanobacteria_moss_seperate -15.68300
## moss_alone-Cyanobacteria_moss_symbiosis -31.58833
## lwr
## Cyanobacteria_moss_seperate-cyano_alone 4.386640
## Cyanobacteria_moss_symbiosis-cyano_alone 20.291973
## moss_alone-cyano_alone -11.296360
## Cyanobacteria_moss_symbiosis-Cyanobacteria_moss_seperate -6.802027
## moss_alone-Cyanobacteria_moss_seperate -38.390360
## moss_alone-Cyanobacteria_moss_symbiosis -54.295694
## upr
## Cyanobacteria_moss_seperate-cyano_alone 49.801360
## Cyanobacteria_moss_symbiosis-cyano_alone 65.706694
## moss_alone-cyano_alone 34.118360
## Cyanobacteria_moss_symbiosis-Cyanobacteria_moss_seperate 38.612694
## moss_alone-Cyanobacteria_moss_seperate 7.024360
## moss_alone-Cyanobacteria_moss_symbiosis -8.880973
## p adj
## Cyanobacteria_moss_seperate-cyano_alone 0.0124514
## Cyanobacteria_moss_symbiosis-cyano_alone 0.0000163
## moss_alone-cyano_alone 0.5581616
## Cyanobacteria_moss_symbiosis-Cyanobacteria_moss_seperate 0.2662823
## moss_alone-Cyanobacteria_moss_seperate 0.2781954
## moss_alone-Cyanobacteria_moss_symbiosis 0.0024067
## Df Sum Sq Mean Sq F value Pr(>F)
## year 1 2465 2465 2.365 0.1269
## pH 2 34698 17349 16.642 4.56e-07 ***
## year:pH 2 6359 3180 3.050 0.0512 .
## Residuals 114 118847 1043
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Df Sum Sq Mean Sq F value Pr(>F)
## year 1 2465 2465 1.819 0.18
## Residuals 118 159905 1355
pH 3.5 t-tests
##
## Welch Two Sample t-test
##
## data: ph3.5_cyano_alone_2017$delta_weight and ph3.5_cyano_alone_2018$delta_weight
## t = 1.7477, df = 3.5496, p-value = 0.1645
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## -15.26223 60.72890
## sample estimates:
## mean of x mean of y
## 1.383333 -21.350000
##
## Welch Two Sample t-test
##
## data: ph3.5_moss_alone_2017$delta_weight and ph3.5_moss_alone_2018$delta_weight
## t = -1.1256, df = 3.8116, p-value = 0.3262
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## -66.18064 28.53064
## sample estimates:
## mean of x mean of y
## 13.825 32.650
##
## Welch Two Sample t-test
##
## data: ph3.5_cmseparate_2017$delta_weight and ph3.5_cmseparate_2018$delta_weight
## t = 0.18795, df = 3.0714, p-value = 0.8626
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## -61.40599 69.22266
## sample estimates:
## mean of x mean of y
## 15.20833 11.30000
##
## Welch Two Sample t-test
##
## data: ph3.5_cmsymbiosis_2017$delta_weight and ph3.5_cmsymbiosis_2018$delta_weight
## t = 2.2001, df = 6.2444, p-value = 0.06835
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## -3.028584 62.568584
## sample estimates:
## mean of x mean of y
## 44.095 14.325
pH 5.5 t-tests
##
## Welch Two Sample t-test
##
## data: ph5.5_cyano_alone_2017$delta_weight and ph5.5_cyano_alone_2018$delta_weight
## t = -0.9411, df = 4.3344, p-value = 0.3961
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## -57.41747 27.68747
## sample estimates:
## mean of x mean of y
## 5.635 20.500
##
## Welch Two Sample t-test
##
## data: ph5.5_moss_alone_2017$delta_weight and ph5.5_moss_alone_2018$delta_weight
## t = -0.2556, df = 7.9984, p-value = 0.8047
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## -34.50996 27.62329
## sample estimates:
## mean of x mean of y
## 32.08167 35.52500
##
## Welch Two Sample t-test
##
## data: ph5.5_cmseparate_2017$delta_weight and ph5.5_cmseparate_2018$delta_weight
## t = -0.76898, df = 6.7714, p-value = 0.4679
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## -74.99429 38.37762
## sample estimates:
## mean of x mean of y
## 37.71667 56.02500
##
## Welch Two Sample t-test
##
## data: ph5.5_cmsymbiosis_2017$delta_weight and ph5.5_cmsymbiosis_2018$delta_weight
## t = -0.17764, df = 4.2255, p-value = 0.8672
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## -67.37097 59.10764
## sample estimates:
## mean of x mean of y
## 55.49333 59.62500
pH 8.5 t-tests
##
## Welch Two Sample t-test
##
## data: ph8.5_cyano_alone_2017$delta_weight and ph8.5_cyano_alone_2018$delta_weight
## t = -1.6909, df = 7.9551, p-value = 0.1295
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## -79.11996 12.21330
## sample estimates:
## mean of x mean of y
## 29.79667 63.25000
##
## Welch Two Sample t-test
##
## data: ph8.5_moss_alone_2017$delta_weight and ph8.5_moss_alone_2018$delta_weight
## t = -0.65332, df = 7.7814, p-value = 0.5324
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## -25.25110 14.14443
## sample estimates:
## mean of x mean of y
## 24.24667 29.80000
##
## Welch Two Sample t-test
##
## data: ph8.5_cmseparate_2017$delta_weight and ph8.5_cmseparate_2018$delta_weight
## t = -1.723, df = 6.472, p-value = 0.132
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## -93.43573 15.42239
## sample estimates:
## mean of x mean of y
## 54.04333 93.05000
##
## Welch Two Sample t-test
##
## data: ph8.5_cmsymbiosis_2017$delta_weight and ph8.5_cmsymbiosis_2018$delta_weight
## t = -2.3212, df = 5.525, p-value = 0.06304
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## -61.988073 2.284739
## sample estimates:
## mean of x mean of y
## 74.77333 104.62500
2017 & 2018 Comparison Figure
## quartz_off_screen
## 2
## quartz_off_screen
## 2
(in progress)
Goal – determine significant changes in metabolites between cyanobacteria and moss using kruskal wallis test.
To look at how suernatant from 1) cyano pellet when incubated with moss supernatant (Ph2-super-Nmusc-SfallaxSupp) compares to 2) moss only supernantant (Ph1-super-Sfallax).
| p.value | met_direction | compound_atlas_ID | label | Identified_metabolite |
|---|---|---|---|---|
| 0.0138744 | uptake_up by cyano | 0130_NADpositive_11p55 | NAD | NAD |
| 0.0138744 | eluted_by cyano | 0001_4-Pyridoxic_acid_positive_1p32 | 4-PYRIDOXATE | 4-PYRIDOXATE |
| 0.0138744 | uptake_up by cyano | 0207_UDP-glucose_negative_11p47 | URIDINE 5’-DIPHOSPHOGLUCOSE | URIDINE 5’-DIPHOSPHOGLUCOSE / URIDINE 5’-DIPHOSPHOGALACTOSE |
| 0.0138744 | uptake_up by cyano | 0208_UDP-D-glucose_negative_11p52 | URIDINE 5’-DIPHOSPHOGALACTOSE | URIDINE 5’-DIPHOSPHOGLUCOSE / URIDINE 5’-DIPHOSPHOGALACTOSE |
| 0.0179605 | eluted_by cyano | 0056_2-Hydroxy-4methylthio_butyric_acid_negative_3p66 | 2-HYDROXY-4-(METHYLTHIO)BUTYRIC ACID | 2-HYDROXY-4-(METHYLTHIO)BUTYRIC ACID |
| 0.0179605 | eluted_by cyano | 0223_L-histidine_negative_13p06 | L-histidine | L-histidine |
| 0.0201646 | eluted_by cyano | 0216_L-histidine_negative_11p85 | L-HISTIDINE | L-HISTIDINE |
| 0.0201646 | uptake_up by cyano | 0230_L-ornithine_negative_18p98 | L-ORNITHINE | L-ORNITHINE |
## [1] "# elluted cyanobacteria metabolites (p.value <= 0.05) is: 65"
## [1] "# taken cyanobacteria metabolites (p.value <= 0.05) is: 79"
Goal – determine significant changes in metabolites between cyanobacteria and moss using kruskal wallis test.
Supernatant changes from 1) suernatant from moss pellet when incubated with cyanobacteria supernatant (Ph2-super-Sfallax-NmuscSupp) compared to 2) cyanobacteria pellet only supernantant (Ph1-super-Nmusc).
| p.value | met_direction | compound_atlas_ID | label | Identified_metabolite |
|---|---|---|---|---|
| 0.0138744 | uptake_up by moss | 0105_cytidine_negative_6p43 | CYTIDINE | CYTIDINE |
| 0.0138744 | uptake_up by moss | 0174_thiamine_negative_10p28 | THIAMINE | THIAMINE |
| 0.0138744 | eluted_by moss | 0226_ANSERINE_negative_14p47 | L-ANSERINE | L-ANSERINE |
| 0.0138744 | uptake_up by moss | 0056_2-Hydroxy-4methylthio_butyric_acid_negative_3p66 | 2-HYDROXY-4-(METHYLTHIO)BUTYRIC ACID | 2-HYDROXY-4-(METHYLTHIO)BUTYRIC ACID |
| 0.0179605 | uptake_up by moss | 0133_xanthosine_negative_8p42 | XANTHOSINE | XANTHOSINE |
| 0.0179605 | eluted_by moss | 0058_DFructose_positive_7p00 | fructose | fructose |
| 0.0201646 | eluted_by moss | 0130_NADpositive_11p55 | NAD | NAD |
| 0.0201646 | uptake_up by moss | 0150_2-Phospho-D-Glyceric_Acid_positive_12p51 | L-2-PHOSPHOGLYCERIC ACID | L-2-PHOSPHOGLYCERIC ACID |
## [1] "# elluted moss metabolites (p.value <= 0.05) is: 103"
## [1] "# taken moss metabolites (p.value <= 0.05) is: 44"
Goal – determine significant changes in metabolites between fungus and cyanobacteria using kruskal wallis test.
Supernatant changes from 1) suernatant from fungus pellet when incubated with cyanobacteria supernatant (Ph2-super-Tacro-NmuscSupp) compared to 2) cyanobacteria pellet only supernantant (Ph1-super-Nmusc).
| p.value | met_direction | compound_atlas_ID | label | Identified_metabolite |
|---|---|---|---|---|
| 0.0138744 | uptake_up by fungus | 0001_4-Pyridoxic_acid_positive_1p32 | 4-PYRIDOXATE | 4-PYRIDOXATE |
| 0.0138744 | uptake_up by fungus | 0011_1-Methyladenosine_positive_2p17 | 1-METHYLADENOSINE | 1-METHYLADENOSINE |
| 0.0138744 | eluted_by fungus | 0218_D-Glycerol_1-phosphate_negative_12p21 | SN-GLYCEROL 3-PHOSPHATE | SN-GLYCEROL 3-PHOSPHATE |
| 0.0138744 | eluted_by fungus | 0142_beta-Glycerophosphoric_acid_positive_11p81 | GLYCEROL 2-PHOSPHATE | GLYCEROL 2-PHOSPHATE / SN-GLYCEROL 3-PHOSPHATE |
| 0.0179605 | uptake_up by fungus | 0082_N-Acetyl-DL-methionine_negative_5p11 | N-ACETYL-DL-METHIONINE | N-ACETYL-DL-METHIONINE |
| 0.0179605 | uptake_up by fungus | 0074_3-METHOXY-L-TYROSINE_positive_8p17 | 3-METHOXY-L-TYROSINE | 3-METHOXY-L-TYROSINE |
| 0.0179605 | uptake_up by fungus | 0005_1-Hydroxy-2-naphthoic_acid_negative_1p14 | 1-HYDROXY-2-NAPHTHOATE | 1-HYDROXY-2-NAPHTHOATE |
| 0.0201646 | uptake_up by fungus | 0150_2-Phospho-D-Glyceric_Acid_positive_12p51 | L-2-PHOSPHOGLYCERIC ACID | L-2-PHOSPHOGLYCERIC ACID |
## [1] "# elluted fungal metabolites (p.value <= 0.05) is: 51"
## [1] "# taken fungal metabolites (p.value <= 0.05) is: 87"
Goal – determine significant changes in metabolites between fungus and moss using kruskal wallis test.
Supernatant changes from 1) suernatant from fungus pellet when incubated with moss supernatant (Ph2-super-Tacro-SfallaxSupp) compared to 2) moss pellet only supernantant (Ph1-super-Sfallax).
| p.value | met_direction | compound_atlas_ID | label | Identified_metabolite |
|---|---|---|---|---|
| 0.0138744 | uptake_up by fungus | 0005_dihydrouracil_positive_1p57 | 5,6-DIHYDROURACIL | 5,6-DIHYDROURACIL |
| 0.0138744 | eluted_by fungus | 0001_4-Pyridoxic_acid_positive_1p32 | 4-PYRIDOXATE | 4-PYRIDOXATE |
| 0.0138744 | eluted_by fungus | 0174_thiamine_negative_10p28 | THIAMINE | THIAMINE |
| 0.0138744 | uptake_up by fungus | 0095_2deoxyguanosine_negative_6p18 | 2’-DEOXYGUANOSINE | 2’-DEOXYGUANOSINE |
| 0.0138744 | uptake_up by fungus | 0083_DIPALMITOYL_CEPHALIN_negative_5p15 | 1,2-DIPALMITOYL-RAC-GLYCERO-3-PHOSPHOETHANOLAMINE | 1,2-DIPALMITOYL-RAC-GLYCERO-3-PHOSPHOETHANOLAMINE |
| 0.0179605 | eluted_by fungus | 0102_Orotic_acid_negative_6p35 | OROTATE | OROTATE |
| 0.0179605 | eluted_by fungus | 0056_2-Hydroxy-4methylthio_butyric_acid_negative_3p66 | 2-HYDROXY-4-(METHYLTHIO)BUTYRIC ACID | 2-HYDROXY-4-(METHYLTHIO)BUTYRIC ACID |
| 0.0201646 | uptake_up by fungus | 0011_1-Methyladenosine_positive_2p17 | 1-METHYLADENOSINE | 1-METHYLADENOSINE |
## [1] "# elluted fungal metabolites (p.value <= 0.05) is: 118"
## [1] "# taken fungal metabolites (p.value <= 0.05) is: 32"
Goal – determine significant changes in metabolites between fungus and moss using kruskal wallis test.
Supernatant changes from 1) suernatant from moss pellet when incubated with fungus supernatant (Ph2-super-Sfallax-TacroSupp) compared to 2) fungus pellet only supernantant (Ph1-super-Tacro).
| p.value | met_direction | compound_atlas_ID | label | Identified_metabolite |
|---|---|---|---|---|
| 0.0138744 | eluted_by moss | 0132_3-Nitro-L-tyrosine_negative_8p33 | 3-NITRO-L-TYROSINE | 3-NITRO-L-TYROSINE |
| 0.0138744 | eluted_by moss | 0146_AICA_ribonucleotide_positive_12p02 | 5-AMINOIMIDAZOLE-4-CARBOXAMIDE-1-BETA-D-RIBOFURANOSYL 5’-MONOPHOSPHATE | 5-AMINOIMIDAZOLE-4-CARBOXAMIDE-1-BETA-D-RIBOFURANOSYL 5’-MONOPHOSPHATE |
| 0.0138744 | eluted_by moss | 0105_S-adenosyl-L-homocysteine_positive_10p36 | S-(5’-ADENOSYL)-L-HOMOCYSTEINE | S-(5’-ADENOSYL)-L-HOMOCYSTEINE |
| 0.0138744 | eluted_by moss | 0134_3-Hydroxy-dl-kynurenine_negative_8p42 | 3-HYDROXYKYNURENINE | 3-HYDROXYKYNURENINE |
| 0.0179605 | eluted_by moss | 0043_2DEOXYURIDINE_negative_2p47 | DEOXYURIDINE | DEOXYURIDINE |
| 0.0179605 | eluted_by moss | 0069_5-Hydroxyindole-3-acetic_acid_positive_7p96 | 5-HYDROXYINDOLEACETATE | 5-HYDROXYINDOLEACETATE |
| 0.0201646 | eluted_by moss | 0130_NADpositive_11p55 | NAD | NAD |
| 0.0201646 | uptake_up by moss | 0162_N-Acetylneuraminic_Acid_negative_9p99 | N-ACETYLNEURAMINATE | N-ACETYLNEURAMINATE |
## [1] "# elluted fungal metabolites (p.value <= 0.05) is: 102"
## [1] "# taken fungal metabolites (p.value <= 0.05) is: 21"
Supernatant changes from 1) suernatant from cyano pellet when incubated with fungus supernatant (Ph2-super-Nmusc-TacroSupp) compared to 2) fungus pellet only supernantant (Ph1-super-Tacro).
2.7.0.0.0.0.0.1 something is wrong with below code
| p.value | met_direction | compound_atlas_ID | label | Identified_metabolite |
|---|---|---|---|---|
| 0.0138744 | eluted_by cyano | 0133_xanthosine_negative_8p42 | XANTHOSINE | XANTHOSINE |
| 0.0138744 | eluted_by cyano | 0132_3-Nitro-L-tyrosine_negative_8p33 | 3-NITRO-L-TYROSINE | 3-NITRO-L-TYROSINE |
| 0.0138744 | eluted_by cyano | 0105_S-adenosyl-L-homocysteine_positive_10p36 | S-(5’-ADENOSYL)-L-HOMOCYSTEINE | S-(5’-ADENOSYL)-L-HOMOCYSTEINE |
| 0.0138744 | eluted_by cyano | 0009_5deoxyadenosine_positive_2p03 | 5’-DEOXYADENOSINE | 5’-DEOXYADENOSINE / 2’-DEOXYADENOSINE |
| 0.0138744 | eluted_by cyano | 0013_2deoxyadenosine_positive_2p42 | 2’-DEOXYADENOSINE | 5’-DEOXYADENOSINE / 2’-DEOXYADENOSINE |
| 0.0138744 | eluted_by cyano | 0074_3-METHOXY-L-TYROSINE_positive_8p17 | 3-METHOXY-L-TYROSINE | 3-METHOXY-L-TYROSINE |
| 0.0138744 | eluted_by cyano | 0223_L-histidine_negative_13p06 | L-histidine | L-histidine |
| 0.0179605 | eluted_by cyano | 0069_5-Hydroxyindole-3-acetic_acid_positive_7p96 | 5-HYDROXYINDOLEACETATE | 5-HYDROXYINDOLEACETATE |
## [1] "# elluted cyano metabolites (p.value <= 0.05) is: 125"
## [1] "# taken cyano metabolites (p.value <= 0.05) is: 25"